As explained on the GSX manual, the number of wagons depends on the estimated passengers on board, which is derived from your loaded cargo in the aircraft configuration (divided by 220 lbs, which is an industry standard to estimate weight of a passenger + luggage).
The number of bags and thus wagons is not 1:1 with reality, otherwise the boarding/deboarding would take way too long and we would need longer trains and lots of bags animations for the larger airplanes. This means with a smaller airplane, it's very much possible and normal you would see less than 3 wagons.